Hello,
First, to get the entropy functionality to work, you need to use nab from
AmberTools 1.4. There are a number of ways you can make sure that it is
compiled with the proper version (such as soft linking the nab from
AmberTools 1.4 into the amber10/bin directory).
As for your other issues. You do not need to export PYTHONPATH for the
basic modules that are included with Python. When you do "sudo make
install", it takes the copy compiled in your local directory where you
extracted the python files and puts everything into /usr/local. It puts
python in /usr/local/bin and all the libraries and such in /usr/local/lib.
The error you're getting is one in which "os" does not exist. However, this
is a standard Python module that comes with every working version of
Python. Therefore, I'm guessing your python installation did not go
properly.
The only thing you actually need to define PYTHONPATH for is mpi4py if you
don't install it in the same directory as the rest of the Python libraries
are installed.
Hope this helps,
Jason
On Sat, Jul 3, 2010 at 7:38 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Amber Experts,
>
>
>
> I could like to install MMPBSA.py. Following the discriptions in the
> tutorial. I do the followings things, but error message at the end of this
> email was encountered. Could you mind to teach me how to get rid of this?
>
>
>
> (1) Download python2.6.5 in my linux workstation. I extract the file in
> /home directory. type "./configure" in /home/python2.6.5 directory. type
> "make", This creates an executable "./python" to install in /usr/local
> directory. Then I type "sudo make install"
>
>
>
> (2) I found Numberic, Numeric.path and README files in the
> /usr/local/lib/python2.6.5/site-packages/ directory.
>
>
>
>
>
> (5) in home directory of the console. I typed
>
>
>
> "export PYTHONPATH=/home/user/lib/python2.6.5/site-packages\:$PYTHONPATH
>
>
>
> (3) When I type python. I see follows:
>
>
> 'import site' failed; use -v for traceback
> Python 2.6.5 (r265:79063, Jul 3 2010, 18:49:13)
> [GCC 4.4.1] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
>
>
>
>
> (5) I "think" python 2.6.5 was installed.
>
>
>
> (6) Then, I process to install MMPBSA.py for serial runs.
>
>
>
> (7) mv mm_pbsa_py.tar.gz $AMBERHOME/src
>
>
>
> (8) tar zxvf mmpbsa_py.tar.gz
>
>
>
> (9) cd $AMBERHOME/src/mmpbsa_py
>
>
>
> (10) make serial clean to make sure it is a clean installation.
>
>
>
> (11) I found following error message when after installation
>
>
>
> ===========================================================================
> /bin/bash setup.sh
> Python version 2 detected. No file conversion necessary.
> 'import site' failed; use -v for traceback
> /bin/cp MMPBSA.py *pyc /home/amber10/bin
> /home/amber10/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.
> nab
> mmpbsa_entropy.nab:58 fld 'ls_method' not in struct 'xo'
> mmpbsa_entropy.nab:58 operator '=': left operand has wrong class.
> mmpbsa_entropy.nab:58 unknown attribute 'ls_method'
> mmpbsa_entropy.nab:59 fld 'ls_maxiter' not in struct 'xo'
> mmpbsa_entropy.nab:59 operator '=': left operand has wrong class.
> mmpbsa_entropy.nab:59 unknown attribute 'ls_maxiter'
> mmpbsa_entropy.nab:60 fld 'ls_maxatmov' not in struct 'xo'
> mmpbsa_entropy.nab:60 operator '=': left operand has wrong class.
> mmpbsa_entropy.nab:60 unknown attribute 'ls_maxatmov'
> nab2c failed!
> make: [install] Error 1 (ignored)
> /bin/mv mmpbsa_py_nabnmode /home/amber10/bin
> /bin/mv: cannot stat `mmpbsa_py_nabnmode': No such file or directory
> make: [install] Error 1 (ignored)
> /bin/rm -f *pyc
> /bin/rm -f mmpbsa_entropy.c
> ===========================================================================
>
>
>
> (15) I saw the executable file MMPBSA.py in the /home/amber10/src/mmpbsa_py
> directory. I then type MMPBSA.py in the same directory
>
>
>
> ===============================================================
>
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
> File "/home/amber10/exe/MMPBSA.py", line 42, in <module>
> import sys, os, time, math # (1)
> ImportError: No module named os
> ================================================================
>
>
>
> (16) I tried to type MMPBSA.py in the /home/amber10/exe directory.
> However, the same error message was found.
>
>
>
> Did I do anything wrong here? Did I miss any important steps. Please
> kindly instruct.
>
>
>
> Best regards,
>
>
>
> Cat
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jul 03 2010 - 08:00:03 PDT
